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Code Block
languagebash
titlelog into lonestar 5 (aka ls5) stampede2 with the ssh command
collapsetrue
ssh <username>@stampede2.tacc.utexas.edu

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Now that we have backed up your profiles so you won't lose any previous settings, you can copy our predefined GVA2022.bashrc file from the /corral-repl/utexas/BioITeam/scriptsgva_course/ folder to your $HOME folder as .bashrc and the predefined GVA2022.profile as .profile from the same location before using the chmod command to change the permissions to read and write for the user only.

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Code Block
languagebash
titleHow to leave Lonestar stampede2 by logout or exit from a remote connection
collapsetrue
logout
# or
exit

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Code Block
languagebash
titleGo log back in to Lonestarstampede2
collapsetrue
ssh <username>@stampede2.tacc.utexas.edu

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Code Block
titleCreating a shortcut to the main Lonestar Stampede2 working directories
cdh
ln -s $SCRATCH scratch
ln -s $WORK work
ln -s $BI BioITeam

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No Format
The following packages will be downloaded:      


    package                    |            build
    ---------------------------|-----------------
    dbus-1.13.18               |       hb2f20db_0         504 KB
    fastqc-0.11.9              |       hdfd78af_1         9.7 MB  bioconda
    font-ttf-dejavu-sans-mono-2.37|       h6964260hd3eb1b0_0         335 KB
    ------------------------------------------------------------glib-2.69.1                |       h4ff587b_1         1.7 MB
    libxml2-2.9.14             |       h74e7548_0  Total:       718 KB
   10 openjdk-11.0.13 MB  The following NEW packages will be INSTALLED:   | fastqc      h87a67e3_0       bioconda/noarch::fastqc-0.11.9-hdfd78af_1341.0 MB
    font----ttf-dejavu-s~ pkgs/main/noarch::font-ttf-dejavu-sans-mono-2.37-h6964260_0
  openjdk-------------------------------------------------------
                                           Total:       354.0 MB  


The following NEW packages will be INSTALLED:    
  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu
  dbus               pkgs/main/linux-64::dbus-1.13.18-hb2f20db_0
  expat              pkgs/main/linux-64::expat-2.4.4-h295c915_0
  fastqc             bioconda/noarch::fastqc-0.11.9-hdfd78af_1
  font-ttf-dejavu-s~ pkgs/main/noarch::font-ttf-dejavu-sans-mono-2.37-hd3eb1b0_0
  fontconfig         pkgs/main/linux-64::fontconfig-2.13.1-h6c09931_0
  freetype           pkgs/main/linux-64::freetype-2.11.0-h70c0345_0
  glib               pkgs/main/linux-64::glib-2.69.1-h4ff587b_1
  icu                pkgs/main/linux-64::icu-58.2-he6710b0_3
  libffi             pkgs/main/linux-64::libffi-3.3-he6710b0_2
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1
  libgomp            pkgs/main/linux-64::libgomp-11.2.0-h1234567_1
  libpng             pkgs/main/linux-64::libpng-1.6.37-hbc83047_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1
  libuuid            pkgs/main/linux-64::libuuid-1.0.3-h7f8727e_2
  libxcb             pkgs/main/linux-64::libxcb-1.15-h7f8727e_0
  libxml2            pkgs/main/linux-64::libxml2-2.9.14-h74e7548_0
  openjdk            pkgs/main/linux-64::openjdk-11.0.13-h87a67e3_0
  pcre               pkgs/main/linux-64::pcre-8.45-h295c915_0
  perl               pkgs/main/linux-64::perl-5.26.2-h14c3975_0
  xz                 pkgs/main/linux-64::xz-5.2.5-h7f8727e_1
  zlib               pkgs/main/linux-64::openjdkzlib-81.02.15212-h7b6447c_3h7f8727e_2
   

Proceed ([y]/n)? y


Downloading and Extracting Packages
fastqc-0.11.9        | 9.7 MB    | ####################################################################################################################################################################################### | 100% 
font-ttf-dejavu-sans | 335 KB    | ####################################################################################################################################################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

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In previous years, the pip installation program was used to install a few programs. While those programs will be installed through conda this year, the link here is provided to give a detailed walk through of how to use pip on TACC resources. This is particularly helpful for making use of the '--user' flag during the installation process as you do not have the expected permissions to install things in the default directories.

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